Related papers: genomepy: genes and genomes at your fingertips
Reproducibility is a crucial aspect of scientific research that involves the ability to independently replicate experimental results by analysing the same data or repeating the same experiment. Over the years, many works have been proposed…
Objectives: The vast and complex nature of human genomic sequencing data presents challenges for effective analysis. This review aims to investigate the application of Natural Language Processing (NLP) techniques, particularly Large…
Summary: TreeGrafter is a new software tool for annotating protein sequences using annotated phylogenetic trees. Cur-rently, the tool provides annotations to Gene Ontology terms, and PANTHER protein class, family and subfamily. The…
Raman spectroscopy is a non-destructive and label-free chemical analysis technique, which plays a key role in the analysis and discovery cycle of various branches of science. Nonetheless, progress in Raman spectroscopic analysis is still…
Microarray is one of the essential technologies used by the biologist to measure genome-wide expression levels of genes in a particular organism under some particular conditions or stimuli. As microarrays technologies have become more…
Biologists who want to analyse their single-cell transcriptomics dataset must install and use specialist software via the command line. This is often impractical for non-bioinformaticians. Whilst the popular CELLxGENE software provides an…
Explosive growth in the amount of genomic data is matched by increasing power of consumer-grade computers. Even applications that require powerful servers can be quickly tested on desktop or laptop machines if we can generate representative…
The advent of high-throughput sequencing technologies has revolutionized genome analysis by enabling the rapid and cost-effective sequencing of large genomes. Despite these advancements, the increasing complexity and volume of genomic data…
Identifying phenotype-associated genes is a common first step in polygenic risk score construction, enrichment testing, target prioritisation and variant interpretation, but relevant evidence is distributed across heterogeneous databases…
Typical personal medical data contains sensitive information about individuals. Storing or sharing the personal medical data is thus often risky. For example, a short DNA sequence can provide information that can not only identify an…
The rapid growth in biological sequence data is revolutionizing our understanding of genotypic diversity and challenging conventional approaches to informatics. With the increasing availability of genomic data, traditional bioinformatic…
Reducing the cost of sequencing genomes provided by next-generation sequencing technologies has greatly increased the number of genomic projects. As a result, there is a growing need for better assembly and assembly validation methods. One…
Motivation: The pan-genome can be stored as elastic-degenerate (ED) string, a recently introduced compact representation of multiple overlapping sequences. However, a search over the ED string does not indicate which individuals (if any)…
The Gene Ontology (GO) project is the largest resource for cataloguing gene function. The combination of solid conceptual underpinnings and a practical set of features have made the GO a widely adopted resource in the research community and…
Multi-omic datasets offer opportunities for improved biomarker discovery in cancer research, but their high dimensionality and limited sample sizes make identifying compact and effective biomarker panels challenging. Feature selection in…
Deep generative models open new avenues for simulating realistic genomic data while preserving privacy and addressing data accessibility constraints. While previous studies have primarily focused on generating gene expression or haplotype…
In the past decade, transcriptome data have become an important component of many phylogenetic studies. Phylogenetic studies now regularly include genes from newly sequenced transcriptomes, as well as publicly available transcriptomes and…
In recent years, the sequencing, assembling and annotation of prokaryotic genomes has become increasingly easy and cheap. Thus it becomes increasingly feasible and interesting to perform comparative genomics analyses of new genomes to those…
Summary: BGT is a compact format, a fast command line tool and a simple web application for efficient and convenient query of whole-genome genotypes and frequencies across tens to hundreds of thousands of samples. On real data, it encodes…
Chromosome analysis is a fundamental step in the diagnosis of genetic diseases, but the manual karyotyping workflow is time-consuming and heavily dependent on expert specialists, often requiring several days per patient. Although Deep…